Global estimates of transmission intensity and short-term forecasts during the COVID-19 pandemic

Challenges, impacts and implications for the future

Sebastian Funk

https://epiforecasts.io

“We were losing ourselves in details […] all we needed to know is, are the number of cases rising, falling or levelling off?”

Hans Rosling, Liberia, 2014

Connection to real-time modelling

  • what is the number of cases? (nowcasting)
  • is the number rising/falling/leveling off (R_t estimation)
  • what are the implications? (forecasting)

The answer to the question is not always obvious

COVID-19

30 January, 2020

Funk et al., cmmid.github.io, 2020

2 March, 2020

Abbott et al., cmmid.github.io, 2020

August 2020

https://epiforecasts.io/covid/posts/global/

Generative Bayesian model

\[ \begin{align} \textrm{New infections}~I(t) & = R_t \sum_{\tau} g_{\tau} I_{t-\tau}\\ \textrm{Reproduction number}~R(t) & = R_{t-1} \exp(\textrm{GP})\\ \textrm{Delayed reporting}~D(t) & = \sum_\tau \xi_\tau I_{t-\tau} \\ \textrm{Observations}~C(t) & = \mathrm{NegBin}(D_t \omega_{(t \textrm{mod} 7)}, \phi) \end{align} \]

Implemented in stan.

EpiNow2 model definition, epiforecasts.io, 2024

High-performance computing

R package for \(R_t\) estimation and forecasting

R package for (sub-)national data

Palmer et al., JOSS, 2021

Subnational estimates

Daily estimates stored on github

Challenges

Challenge #1: Methodology

Originally used methodology that ignored delays.

Gostic et al., PLOS Comp Biol, 2020

Challenge #2: Lack of local context

Abbott et al., Wellcome Open Res, 2020

Challenge #3: Communication

Challenge #4: Multiplication of effort

Brockhaus et al., PLOS Comp Biol, 2023

Challenge #5: Capacity

Impact

Impact #1: Use by other researchers

Impact #2: Use by ourselves

Davies et al., Science, 2021

Abbott et al., medRxiv, 2021

Sheratt et al., Proc Roy Soc B, 2021

Impact #3: Use in public health agencies

“The Rt estimates generated by the EpiForecasts team were used extensively by the WHO COVID-19 Analytics unit. They formed a core part of two routine analysis pipelines […] regularly presented to the incident management structure at WHO headquarters, including senior management, as well as regional and national WHO offices.”

Future directions

Tools as route towards localised work

Tool development for epidemic preparedness

How do we assess value of modelling work?

  • Quality
  • Relevance
  • Communication

Workshop at WHO Hub Berlin (8-9 October, 2024)

“We were losing ourselves in details […] all we needed to know is, are the number of cases rising, falling or levelling off?”

Hans Rosling, Liberia, 2014

Thank you

For more detail:

Abbott & Funk, 2022, Reflections on two years estimating effective reproduction numbers

Slides at https://epiforecasts.io/slides/ini_20240805.html